WASHINGTON — The team of F.B.I. agents arrived in Iraq to investigate a shooting involving a private company that provided security for Americans in a war zone. It was October 2007, and the name of the company — Blackwater Worldwide — did not yet mean anything to the agents. But what they found shocked them.

Witnesses described a convoy of Blackwater contractors firing wildly into a crowded traffic circle in Baghdad the previous month, killing 17 people. One Iraqi woman watched her mother die as they rode the bus. Another died cradling the head of her mortally wounded son.

“This is the My Lai massacre of Iraq,” one agent remembers John Patarini, the team’s leader, saying as they were heading home.

That shooting in Nisour Square, along with the massacre by Marines of 24 Iraqi civilians at Haditha and the abuses at Abu Ghraib prison, became a signature moment in the Iraq war. Five Blackwater security guards were indicted on manslaughter and weapons charges, and a sixth entered a plea deal to testify against his former colleagues.

But over the years, a case that once seemed so clear-cut has been repeatedly undermined by the government’s own mistakes.

Prosecutors are trying to hold together what is left of it. But charges against one contractor were dropped last year because of a lack of evidence. And the government suffered another self-inflicted setback in April when a federal appeals court ruled that the prosecution had missed a deadline and allowed the statute of limitations to expire against a second contractor, Nicholas A. Slatten, a former Army sniper from Tennessee who investigators believe fired the first shots in Nisour Square. A judge then dismissed the case against Mr. Slatten.

The appeals court unanimously rejected the argument that letting Mr. Slatten walk free would be a miscarriage of justice. If such an injustice occurred, the court said, it was caused by the government’s delays, which the court called “inexplicable.”

The Justice Department responded Friday by charging Mr. Slatten with first-degree murder, which has no statute of limitations but carries a much heftier burden of proof.

The trial will renew focus on an episode that inflamed anti-American sentiment abroad and helped cement the image of Blackwater, whose security guards were involved in scores of shootings, as a trigger-happy company that operated with impunity because of its lucrative contracts with the American government.

Now known as Academi, the company was sold by its founder, Erik Prince, to a group of private investors three years after the Nisour Square killings.

But the difficulty the government has had in making a case against the former employees is likely only to reinforce the impression that American contractors were not subject to any rules in Iraq, despite the Obama administration’s attempts to allay Iraqi concerns about the case and Vice President Joseph R. Biden Jr.’s expression of his “personal regret” for the shooting.

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Nicholas A. Slatten, a contractor, in 2008. Accused of firing the first shots, he faces a new charge of first-degree murder.CreditDouglas C. Pizac/Associated Press

“As citizens, we need to ask why our government fails to achieve any accountability for such blatant wrongdoing,” said Susan Burke, a lawyer who represented Iraqi victims of the Nisour Square shooting in a lawsuit that Blackwater settled by paying an undisclosed amount. “The ongoing delays and mistakes undermine any confidence in the system.”

When the F.B.I. team arrived home from Iraq in 2007, court testimony and interviews show, members believed they had the makings of a strong case. Witnesses told a horrific tale, and while Blackwater guards said the shooting had begun with an ambush by insurgents, American military officials told investigators that there had been no sign of such an attack. Even if there had been, the military said, firing grenade launchers in such a crowded space was excessive.

“It was an investigation into the protection of basic human rights that should be afforded to all people, not just citizens of the United States,” Joseph Persichini Jr., the assistant F.B.I. director then in charge of the Washington field office, said in 2008.

But from the beginning, investigators said, they felt their case was being undermined. A State Department security agent reported that, shortly after the shooting, his colleagues had gathered up shell casings, trying to clean up the scene to protect Blackwater. The agent, David Farrington, recalled a meeting in which other State Department officials said, “We’ve got enough to get these guys off now,” according to court testimony.

State Department investigators also gave limited immunity to the Blackwater contractors in exchange for statements about the shooting. After someone leaked those statements to reporters,the investigators tried to make sure that none of their witnesses were influenced by those statements, which could not be used as evidence.

Still, the F.B.I. remained confident. “We already had enough evidence to show that we could work off of the physical evidence,” Mr. Patarini said in court. “The fragments, the casings, the witnesses.”

A key development came in 2008 when one of the guards, Jeremy P. Ridgeway, pleaded guilty to voluntary manslaughter, admitting that he and his colleagues had fired unprovoked on unarmed civilians. That admission was made public the same day that prosecutors in Washington announced manslaughter and weapons charges against the five Blackwater contractors.

But a year later, the case appeared to be all but lost. A federal judge dismissed the charges, citing the Justice Department’s “reckless” behavior. The judge found that, among other things, the prosecutors Kenneth Kohl and Jonathan Malis had distorted evidence and violated the constitutional rights of the defendants.

In response, the Justice Department replaced its prosecution team, which became the subject of internal investigations. And in an unusual move that reflected the diplomatic sensitivities of the case, Mr. Biden personally announced, on a trip to Iraq, that the government would appeal. “A dismissal is not an acquittal,” he said.

An appeals court later reinstated the case against four of the guards, but not Mr. Slatten, whose case prosecutors acknowledged was tainted. They said they planned to charge him again using untainted evidence.

But that did not happen in time, and in September 2012, the five-year statute of limitations for manslaughter expired.

Mr. Slatten is scheduled to be arraigned Monday on the new first-degree murder charge, and prosecutors say they want him to be tried next month alongside his former colleagues. His defense lawyer is expected to oppose that, which could delay the case further.

With or without Mr. Slatten, the case against the three remaining guards is set finally to go to trial, with Mr. Ridgeway as a likely key witness, and the government ready to paint a fearsome picture of a company that became an arm of the United States war effort in Iraq.

A version of this article appears in print on , on Page A1 of the New York edition with the headline: Trying to Salvage Remains of Blackwater Case. Order Reprints | Today’s Paper | Subscribe